How did he manage to pull this off? It's not much of a secret. He knew what he was writing about and that gives him an unfair advantage over most other science journalists.

Let me show you what I mean. Here's John Timmer's profile on the Ars Technica website.

John is Ars Technica's science editor. He has a Bachelor of Arts in Biochemistry from Columbia University, and a Ph.D. in Molecular and Cell Biology from the University of California, Berkeley. John has done over a decade's worth of research in genetics and developmental biology at places like Cornell Medical College and the Memorial Sloan-Kettering Cancer Center. He's been a speaker at the annual meeting of the National Association of Science Writers and the Science Online meetings, and he's one of the organizers of the Science Online NYC discussion series. In addition to being Ars' science content wrangler, John still teaches at Cornell and does freelance writing, editing, and programming.

See what I mean? He has a degree in biochemistry and another one in molecular biology. People like that shouldn't be allowed to write about the ENCODE results because they might embarrass the scientists.

Here's an example from his article ...

This brings us to the ENCODE project, which was set up to provide a comprehensive look at how the human genome behaves inside cells. Back in 2007, the consortium published its first results after having surveyed one percent of the human genome, and the results foreshadowed this past week's events. The first work largely looked at what parts of the genome were made into RNA, a key carrier of genetic information. But the ENCODE press materials performed a sleight-of-hand, indicating that anything made into RNA must have a noticeable impact on the organism: "the genome contains very little unused sequences; genes are just one of many types of DNA sequences that have a functional impact."

There was a small problem with this: we already knew it probably wasn't true. Transposons and dead viruses both produce RNAs that have no known function, and may be harmful in some contexts. So do copies of genes that are mutated into uselessness. If that weren't enough, just a few weeks later, researchers reported that genes that are otherwise shut down often produce short pieces of RNA that are then immediately digested.

So even as the paper was released, we already knew the ENCODE definition of "functional impact" was, at best, broad to the point of being meaningless. At worst, it was actively misleading.

But because these releases are such an important part of framing the discussion that follows in the popular press, the resulting coverage reflected ENCODE's spin on its results. If it was functional, it couldn't be junk. The concept of junk DNA was declared dead far and wide, all based on a set of findings that were perfectly consistent with it.

Four years later, ENCODE apparently decided to kill it again.

There's lots more where that came from. Here's his conclusion ...

More generally, the differences among non-coding DNA, regulatory DNA, and junk DNA aren't really that hard to get straight. And there's no excuse for pretending that things we've known for decades are a complete surprise.

Unfortunately, this is a case where scientists themselves get these details wrong very often, and their mistakes have been magnified by the press releases and coverage that has resulted. That makes it much more likely that any future coverage of these topics will repeat the past errors.

If the confused coverage of ENCODE has done anything positive, it has provoked a public response by a number of scientists. Their criticisms may help convince their colleagues to be more circumspect in the future. And maybe a few more reporters will be aware that this is an area of genuine controversy, and it will help them identify a few of the scientists they should be talking to when covering it in the future.

It's just a shame the public had to be badly misled in the process.

BRAVO John Timmer! Well done, even if you did have an unfair advantage.

Unfortunately, this is a case where scientists themselves get these details wrong very often, and their mistakes have been magnified by the press releases and coverage that has resulted. That makes it much more likely that any future coverage of these topics will repeat the past errors.

I'd like to know if the scientists would agree that what they said were "mistakes". One assumes that they have, at least, similar professional competence in this area as those who COMPETENTLY disagree with them. For the rest of us, who are we supposed to believe? I always remember what Lewontin said:

First, no one can know and understand everything. Even individual scientists are ignorant about most of the body of scientific knowledge, and it is not simply that biologists do not understand quantum mechanics. If I were to ask my colleagues in the Museum of Comparative Zoology at Harvard to explain the evolutionary importance of RNA editing in trypanosomes, they would be just as mystified by the question as the typical well-educated reader of this review.

and

But when scientists transgress the bounds of their own specialty they have no choice but to accept the claims of authority, even though they do not know how solid the grounds of those claims may be. Who am I to believe about quantum physics if not Steven Weinberg, or about the solar system if not Carl Sagan? What worries me is that they may believe what Dawkins and Wilson tell them about evolution.

And if the authorities disagree? In this case I'd be skeptical of claims that rest on definitions of "functional" and "useless". It's clear that the meaning of both of those, in this argument, are contingent on present day knowledge. Basing any kind of definitive conclusion on such contingencies is a big mistake. Especially in an ideological war. The scientists who made grand pronouncements out of the speculations of scientists concerning evolution have provided the opponents of science some of their more successful material. Yet, with that history of the counterproductive effects of ideology masquerading as science, it's more popular as ever. Who is acting foolishly in that?

It's clear that the meaning of both of those, in this argument, are contingent on present day knowledge. Basing any kind of definitive conclusion on such contingencies is a big mistake.

Would you say the same about the conclusion that the Earth orbits the Sun? A definitive conclusion is merited by definitive evidence. So your deduction that the assessment of "junk" must be a contingent one depends on the state of the evidence. And you, sir, in spite of having had evidence and discussion of that evidence in this very blog recommended to you, have apparently not sought it out. Let me recommend it to you once again. I'm sure a decently constructed Google search will find it.

Not all contingencies are equal. That the Earth orbits the sun is less contingent than that whatever percentage of DNA commonly identified as being "junk" remaining constant. Or what has this series of posts been all about. That is the Earth orbiting the sun in the most conventional definition of that idea.

Are you saying that, clearly far from unanimous, POV expressed here is as reliable as the idea that the Earth revolves around the sun?

I haven't made any deductions about this issue other than to express skepticism that something believed to be non-functional today will never be discovered to have a well-defined function in the future. I'm as indifferent to the existence of "junk" DNA as I am to the existence of the Higgs boson. I figure there's not much to be done about it, either way.

Anyone who thinks this argument can tell you anything about "design" is naive. I doubt that a single person would change their position on that question based on the outcome of this issue, and I doubt there ever will be an outcome to it. Or do you expect a mass conversion of atheists if the junk is functional? I doubt it as much as I expect 99% of DNA being condemned as junk would convert a single creationist.

Come on, it's not rocket science. Just read Birney's blog and it's clear that no one is actually disagreeing about the facts - the disagreement is just about the spin and about whether it's a good idea to redefine "functional" to mean something completely unrelated to the everyday meaning of the word.

Are you saying that, clearly far from unanimous, POV expressed here is as reliable as the idea that the Earth revolves around the sun?

I haven't made any deductions about this issue other than to express skepticism that something believed to be non-functional today will never be discovered to have a well-defined function in the future.

Once again I'm asking that you accumulate more information before taking a position. Reading posts from this blog (and some posts by T. R. Gregory as well) will help you understand just how huge the proportion is of human DNA that almost certainly has no function, but is nevertheless transcribed, and how that ties in so fundamentally to the discussions now taking place about ENCODE.

Right now, you're stating conclusions about a controversy without really understanding the basis of either side of it. Maybe you get off on arguing even in the absence of knowledge. I get off on learning.

We need more science journalists who actually have a strong science background. What's ironic about all the crowing from the ID crowd is that all this useless transcription shows how much waste there is in biology. This is further evidence that evolution is unguided and historically contingent.

Matt G, it is evidence of nothing, whatsoever, that evolution is unguided or guided. If you want to claim Junk DNA as evidence of your position, it will never work for it anymore than the stupid claims of "missing links" always to be found, proposed by your ideological ancestors in the late 19th century have been. I'll predict that even if you guys win this round, many "functions" for parts of the proposed junk pile will be continually being found, turning this into a perpetual brawl.

Reviewing the literature surrounding this brawl in its earliest decades, it's impressive how much of the field of battle has not changed one bit, quite often based on outsized claims made by scientists.

Allow me to rephrase, Thought Criminal. These results give us more reason to reject the "Design 'Hypothesis'" and to favor the null hypothesis which is that evolution is unguided. If a dropped ball falls to Earth, do you see that as a guided or an unguided event? Your position suggests that this cannot be determined.

I gather that you see this this as your side against the scientists. Are you acknowledging that your side is not scientific?

Your conclusion is based on your preexisting assumptions, you see what you expect to see. Someone who expects to see design will see design.

I gather that you see this this as your side against the scientists. Are you acknowledging that your side is not scientific?

And this confirms it. You see what you are predisposed to see instead of what's there on the screen as I wrote it. I don't take "a side" in whether or not any part of DNA is "functional" or "junk". I have always held that questions of teleology and "design" are not answerable by science. Science cannot satisfy the ID industry and it, also, won't provide atheists with their greatest desire, which doesn't seem to be valid science but the final nail in the coffin of God. Francis Crick's son said that burying vitalism was his father's great quest, one that he failed. Science can't provide it anymore than it can whether team A or team B is the more awesomely wonderful or if Molson is better than Guinnes.

Read what you just posted, and then read it again. If your irony meter doesn't go off, you need a new one. What's that saying about the beam in your own eye...? Pretending to be above the fray in this matter is neither noble nor intellectually honest - there is no reason to think that evolution is guided. Let me ask you a straightforward question: Do you think ID is science? Another saying you bring to mind is the one about he who doth protest too much.

I don't have an irony meter you want to talk to Negative Entropy about that. Though, I'd think "meter" is probably an exaggeration. Not to mention "irony".

Of course ID isn't science, anyone who understood what I said would know I don't think ID is science. How many times do I have to say SCIENCE CAN'T DEAL WITH THE CONCEPT OF A CREATOR, IT CAN'T DEAL WITH QUESTIONS OF TELEOLOGY OR DESIGN. i'VE SAID THAT FROM THE FIRST TIMES I EVER ADDRESSED THIS STUPID IDEOLOGICAL WAR.

OK, now we're getting somewhere. So then you accept the null hypothesis that there is no design and no designer? I hesitate in using the word hypothesis, and perhaps should say that there is no reason to accept the existence of design and a designer. We agree?

I have always held that questions of teleology and "design" are not answerable by science.

Then you have always been wrong.

Let me introduce you to the Thermos joke:

Three friends are having a spirited discussion about what is the greatest invention of all time. One says fire. A second says the wheel. The third says the Thermos.

The other two ask him how he could ever propose the humble Thermos for inclusion in such august company. He replies, "If you put something cold in it, it stays cold. If you put something hot in it, it stays hot." "Yes, yes," his friends say, "but so what?" He looks at them for a long moment and says:

"But how does it know?"

So - teleology or insulation? Science can plainly answer. Please provide the principle that prevents the same from being true regarding whether teleology or scientifically explainable non-teleological principles are the source of species' characteristics.

Jud, that's a great joke. But allow me to introduce an analogy.Let's say the people in the paintings of George Seurat are 'alive'. They can think, and they can communicate with each other. They have considered their physical make-up, and have concluded that they are an ingenious, intricate system of small points of color. All these points are essentially the same, but in the manner they are arranged they make it possible for all the different people to exist, their surroundings, everything. They marvel at this discovery. But one of them feels that there must be more to their existence than just elemental points of color that happen to behave in such a way as to give rise to, them. He intuits that there must have been some planning involved in how they happened to come about, so well defined and well organized. Okay, how? - the others ask him. 'I don't know, but I just feel that this creator would have to possess powers beyond our own, and operate outside of our own known science." These painted people are stuck in place and time. They have no notion of movement, so the possibility of someone painstakingly planning out the scheme of the painting, and placing each point on the canvas where he wanted it to be, is not even imaginable to them.You are crazy, and deluded, they tell him. 'There is NO evidence that what you are saying is anything more than a meaningless fantasy!"

So then you accept the null hypothesis that there is no design and no designer? Matt

Give me strength. I DON'T REJECT "the null hypothesis". That SCIENCE can't deal with something is no guarantee that it isn't true. Science can't establish with the fact that I started school the year and date I did, but it is a fact that is as absolute as any. Science isn't the measure of all reality, it is only a method to try to discover some kinds of information about the physical universe. The only part of the physical universe it can tell you about are those aspects that can be studied with its methods and tools. Whatever doesn't fit into the methods and tools of science eludes its abilities. Most of reality eludes the abilities of science.

Furthermore, since I reject the idea that science can deal with questions of God or teleology and design in nature, I would reject the attempt to frame questions about that as scientific "hypotheses". That inability prevents statements about those being scientific hypotheses.

Jud, if you think your mind is like a thermos bottle, you're the best judge of your own mind, not me. Though with enough examples of that kind of thinking expressed by materialists it makes me wonder if they are expressing something about their experience of thinking when they represent it in such terms. Which might explain why you guys can't understand points such as the one I just made to Matt. Maybe I should just accept that materialists aren't especially deep thinkers. Maybe they should have thought through more philosophy.

In any case, designing and making thermos bottles are as obvious an instance of intelligent design to achieve a purpose as you could have stumbled on. But what part of science do you use to know that? I know it by reading about how they were made, I may have read an encyclopedia article about the history of thermos bottles (in print, not online) when I was young, though I don't remember it, specifically.

I will point out, as well, that, if you propose the thermos as an analogy from the universe and the designer for God, then the thermos is hardly inclusive of the natural universe. The people who designed it and made it were not performing a random act in nature but were, in fact, intelligently designing and making something, and people are not God. Your opponents would be completely correct if they point out that your joke was a way in which people could ignore obvious intelligent design and performance for something which is taken for being a mere act of nature with no design involved. Which would require me to point out a few different problems of going from thermos to universe, if the more callow among them wanted to go past what the analogy can tell you.

Jud, if you think your mind is like a thermos bottle yada, yada, yada....

Nice way to miss the point and avoid the question. So I'll try asking one more time, and then, since as I said I'm in this to learn, give up on the likelihood of discussions with you leading to any knowledge.

What is the principle on which you base your position that science cannot discern whether teleology or natural principles are responsible for differences among species, when science is clearly adequate to the task of distinguishing between the results of teleology and natural principles in other fields?

I don't know why I should put a lot of effort into this when you can't see the problems with your thermos bottle analogy. So I'll knock off an answer.

Science as an activity consists of observing THE PHYSICAL UNIVERSE, of quantifying what it observes, of analyzing the results of that observation and measurement to come up with a description of the PHYSICAL phenomena that can be logically arrived at from those. It then publishes that analysis so others can look at the account for flaws and for possible replication to see if the same results are arrived at. Though, these days, the theoretical pondering of that seems to want to have an assumed validity on its own, without verification in evidence, I think that's a really stupid idea.

Science can only describe what's there or what would happen if you did something to what's there. It can't tell you where what's there came from, ultimately. It can't tell you how life actually arose on Earth, it can't tell you how the universe came into being. Physical evidence of sufficient detail isn't available, reliable measurements can't be made to address that absent evidence. It can't tell you if the universe is designed or the result of mere chance. It can only tell you what it can, though scientists, and self-appointed champions of science, who are really just ideologues, can pretend it can.

Discerning the mind of God is not within the abilities of science.

Science is an entirely human invention and activity. It is based in logic and mathematics which can't account for their absolute foundations in the terms of those human activities. Science, dealing with far more complex phenomena than numbers is even less able to establish that absolute foundation. As one mathematician pointed out the year before last, some theoretical physicists seem to just want to throw up their hands and pretend that they've achieved that without having done so.

I'm convinced that evolutionary science being hijacked by ideological atheists in the 19th century who claim ownership of it in their emotional rants about religion have done a lot of damage to the science, which suffers whenever someone wants to insert non-scientific content into it. I think the ideology of materialism is responsible for a lot of the trouble science has gotten into. And it was entirely unnecessary. Of course, the conceit and arrogance of scientists making over-sized claims about their abilities had more than a little to do with it.

I'm really coming to believe that materialists are uniformly shallow thinkers who can't see past their own noses. I didn't think that before I was exposed to their thinking, by the thousands, online.

Though, these days, the theoretical pondering of that seems to want to have an assumed validity on its own, without verification in evidence, I think that's a really stupid idea.

Science can only describe what's there or what would happen if you did something to what's there. It can't tell you where what's there came from, ultimately. It can't tell you how life actually arose on Earth, it can't tell you how the universe came into being. Physical evidence of sufficient detail isn't available....

This is a picture of scientific activity that would be unrecognizable to scientists, but might ring true to someone who him- or herself never bothers to find out what "verification in evidence" lies behind the theories.

I note that you still haven't bothered even to read the relevant posts in this very blog on the subject of "junk DNA." So you seem to be exactly the sort of person who never bothers to learn what evidentiary verification there is, then complains of the lack of it. I can certainly see where many scientific issues would seem incapable of solution to you.

Meanwhile, those of us who aren't so lazy will have the enjoyment of learning about the fascinating evidence and solutions that pass you by.

He intuits that there must have been some planning involved in how they happened to come about, so well defined and well organized. Okay, how? - the others ask him. 'I don't know, but I just feel that...

My problem with this is that it elevates intuition to the level of reason.

People intuit all kinds of things. "I just know the Jews were behind 9/11." "I just know Obama is not a citizen."

People throughout history have intuited all kinds of dumb things that lead to huge crimes or mass murder.

If you want national policy based on fact-claims, you better have evidence to back up your fact-claims.

This is a picture of scientific activity that would be unrecognizable to scientists, but might ring true to someone who him- or herself never bothers to find out what "verification in evidence" lies behind the theories.

You seem to have missed this:

We seem to be at a critical point in the history of science, in which we must alter our conception of goals and of what makes a physical theory acceptable. It appears that the fundamental numbers, and even the form, of the apparent laws of nature are not demanded by logic or physical principle. The parameters are free to take on many values and the laws to take on any form that leads to a self-consistent mathematical theory, and they do take on different values and different forms in different universes.

Hawking-Mlodinow

Show me where they had their membership cards as scientists in good standing revoked.

There is zero, absolutely not a single shred of evidence of what the original life form on Earth was like so anything that is said about that is not based in evidence. Unlike the massive evidence of evolution that compels acceptance by a non-Darwinist, such as me, there is absolutely none to support any position about the origin of life. Though I, actually, agree with some of the assumptions about that which Darwin accepted. I believe that there was one, original organism from which all known terrestrial life is descended and that its descendants changed over time to produce the diversity of life. But that's a belief derived from science, it isn't science.

I read enough of the posts about "junk DNA" to ask the question of how anyone knows that the "junk" doesn't have a function that will be discovered someday. It is a stupid, ideological struggle, not a scientific debate.

Science is based on human observation, human mathematics and human logic all based in human experience. All three of those have known limits just as human beings have limits. The limits of mathematics and logic have attained the status of being mathematically and logically proven. Science cannot escape the limits of its methods. It cannot, for example, escape from its reliance on mathematics and logic to assert the existence of another universe that has "different" mathematics and logic, telling us what that could possibly mean through our mathematics and logic. It cannot say whether or not the physical basis it is made to study is as it is and operates as it does by divine intention. It can't stand outside of its physical limits to address that question. Assertions made to that effect can't be "known" in the way that a chemical reaction of known character can be known, it can only be disbelieved or believed or an agnostic position can be taken. Science isn't able to produce more than support for agnosticism on that point.

The study of the visible universe may be said to start with the determination to use our eyes. At the very beginning there is something which might be described as an act of faith – a belief that what our eyes have to show us is significant. I think it can be maintained that it is by an analogous determination that the mystic recognises another faculty of consciousness, and accepts as significant the vista of a world outside space and time that it reveals. But if they start alike, the two outlets from consciousness are followed up by very different methods; and here we meet with a scientific criticism which seems to have considerable justification. It would be wrong to condemn alleged knowledge of the unseen world because it is unable to follow the lines of deduction laid down by science as appropriate to the seen world; but inevitably the two kinds of knowledge are compared, and I think the challenge to a comparison does not come wholly from the scientists. Reduced to precise terms, shorn of worlds that sound inspiring but mean nothing definite, is our scheme of knowledge of what lies in the unseen world, and of its mode of contact with us, at all to be compared with our knowledge (imperfect as it is) of the physical world and its interaction with us? Can we be surprised that the student of physical science ranks it rather with the vague unchecked conjectures in his own subject, on which he feels it his duty to frown? It may be that, in admitting that the comparison is unfavourable, I am doing an injustice to the progress made by systematic theologians and philosophers; but at any rate their defence had better be in other hands than mine.

Although I am rather in sympathy with this criticism of theology, I am not ready to press it to an extreme. In this lecture I have for the most part identified science with the physical science. This is not solely because it is the only side for which I can properly speak. But because it is generally agreed that physical science comes nearest to that complete system of exact knowledge which all sciences have before them as an ideal. Some fall far short of it. The physicist who inveighs against the lack of coherence and the indefiniteness of theological theories, will probably speak not much less harshly of the theories of biology and psychology. They also fail to come up to his standard of methodology. On the other side of him stands an even superior being – the pure mathematician – who has no high opinion of the methods of deduction used in physics, and does not hide his disapproval of the laxity of what is accepted as proof in physical science. And yet somehow knowledge grows in all of these branches. Wherever a way opens we are impelled to seek by the only methods that can be devised for that particular opening, not over-rating the security of our finding, but conscious that in this activity of mind we are obeying the light that is in our nature.

Diogenes, I basically agree with what you write. My analogy was presented as just that, and analogies only go as far as they do. Certainly, even in the fanciful case of the people in the Seurat painting, I would never say the people should decide to follow the one with the intuition, whether by making him a guru or a king.I just think it's important, and I imagine you agree, for everyone, whether scientist or poet, to recognize that this universe is hardly finished revealing itself to us humans. There is still so much we don't understand. There will always be some people who glimpse aspects of these things that are unknown, so I think it is worthwhile to be tolerant of them.They are often wrong, to be sure. The man in the painting could have also 'intuited' that the points of color were the footprints of little dancing elves and fairies.

"Science can only describe what's there or what would happen if you did something to what's there. It can't tell you where what's there came from, ultimately. It can't tell you how life actually arose on Earth, it can't tell you how the universe came into being. Physical evidence of sufficient detail isn't available, reliable measurements can't be made to address that absent evidence. It can't tell you if the universe is designed or the result of mere chance. It can only tell you what it can, though scientists, and self-appointed champions of science, who are really just ideologues, can pretend it can.

Discerning the mind of God is not within the abilities of science.

Science is an entirely human invention and activity."

Who or what is this "God" thing that you asserted? Do you have a method that is better than science for determining that this "God" thing exists and has a mind? Can you discern "the mind of God"? If so, how, and if not then how do you know that "discerning the mind of God is not within the abilities of science"?

What if there are non-human beings on other plants that invented and do science in their neck of the universe? If they exist, and do science, do you know that they are not able to tell where things came from ultimately, or how life arose on their planet or other planets (or even throughout the universe), or how the universe came into being, or whether the universe was designed or the result of mere chance? And where does it say that humans have exhausted all avenues of scientific discovery? Just because humans don't know all the answers to all the questions right now doesn't mean that humans never will know any or all of them.

Will you elaborate on exactly what you mean by "mere chance"? Are design by the "God" thing or "mere chance" the only two choices?

TTC also said: "I'm really coming to believe that materialists are uniformly shallow thinkers who can't see past their own noses."

You're the one putting arbitrary limits on science's abilities to "tell".

"Most of reality eludes the abilities of science."

Such as? On what basis do you say "most"? And what makes you think that most of reality will always elude science (science's "abilities")? Define "reality" and name some things in what you call "reality" that are outside the "abilities" of science.

There was a paper a few years ago where they deleted about 2 Mb of mouse DNA and found the mice with the homozygous deletion were perfectly normal. It would interesting to see what "functional" elements the ENCODE data shows in the corresponding human region.

This is really the core of the argument in regards to ID. The creationists I talk to all don't recognise similarities in DNA between species as evidence of common ancestry because ""As there are similarities between cars made by Ford; so to can different species have similarity"

Obviously my view (and the evidence) disagrees with that because we see the broken pieces of their genome also shared which would not be the case with cars and other ID systems.

The ENCODE data will be central to settling this though. Even if their 80% 'rant' is hyperbole or not. If further experiments (+ past ones) show that these 'biochemical functions' are redundant to making a human a human or a rabbit a rabbit then it settles the common ancestry 'debate' . Of course as mentioned elsewhere they'll ignore that and continue to spit the 80% figure ;)

You can delete lots of known functional genes in mice and the homozygotes are perfectly normal. This was a standard fear of early mouse gene knockout researchers: you'd do all this work to develop a mouse with your favorite gene deleted and nothing would happen. Plenty of examples of that.

There is a new paper that is relevant to the junk DNA skirmish. 29 Mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome.http://www.ncbi.nlm.nih.gov/pubmed/18085818They looked at conserved functional elements to see how many came originally from transposon DNA. They found a lot, but it still only amounts to about 10% of the transposon number in the human genome.Transposons are about half the genome, so this potentially involves about 5% of the genome. However, the actual DNA in the elements identified is only about 7 Mb or about 0.2% of the genome. These are conserved functional elements, and there are presumably species specific, or at least primate- specific elements that wouldn't be included, but the total is still a very small fraction of the genome.

If Timmer is so good, then you must also accept his conclusion: ENCODE remains a phenomenally successful effort, one that will continue to pay dividends by accelerating basic science research for decades to come.

Somehow I doubt that you do, based on your previous comments that ENCODE has provided nothing of fundamental importance,

I agree that ENCODE is a great atlas of data, like Tycho Brahe's catalogs of stars and planet movements. But Tycho Brahe's catalogs were not hypothesis-driven science. Kepler and Newton took that data and did hypothesis-driven science.

I'm not putting down science that's not hypothesis-driven, and I'm not putting down ENCODE. I'm just saying it's not hypothesis-driven science, but it was sold to the Muggles (non-scientists) as hypothesis-driven: thus they needed to concoct a ridiculous story-- about overturning the Junk DNA hypothesis!

It seems Timmer is engaging in some sleight of hand of his own. Notice how he uses the phrase 'noticable impact", where he quotes Encore saying 'functional impact'. Different animals.

So are we to conclude that 'noticeability' is a pre-requisite for functionality?

Timmer is obviously one of those 'out of sight, out of mind' 'conceptualists'.

Maybe thats why he switched from research to journalism.

Timmer: "But the ENCODE press materials performed a sleight-of-hand, indicating that anything made into RNA must have a noticeable impact on the organism: "the genome contains very little unused sequences; genes are just one of many types of DNA sequences that have a functional impact."

While it probably would have been better if Timmer had used "functional" instead of "noticeable", they aren't necessarily different animals. A function should be noticeable, especially if the function affects or changes the organism.

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.